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GeneBe

rs1800630

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The variant allele was found at a frequency of 0.144 in 151,842 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: 𝑓 0.14 ( 1698 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: -2.77
Variant links:

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ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 6-31574699-C-A is Benign according to our data. Variant chr6-31574699-C-A is described in ClinVar as [protective]. Clinvar id is 12390.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21898
AN:
151724
Hom.:
1699
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.109
Gnomad AMI
AF:
0.0297
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.161
Gnomad SAS
AF:
0.257
Gnomad FIN
AF:
0.162
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.156
Gnomad OTH
AF:
0.163
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21905
AN:
151842
Hom.:
1698
Cov.:
31
AF XY:
0.146
AC XY:
10802
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.109
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.148
Gnomad4 EAS
AF:
0.161
Gnomad4 SAS
AF:
0.256
Gnomad4 FIN
AF:
0.162
Gnomad4 NFE
AF:
0.156
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.153
Hom.:
2867
Bravo
AF:
0.141
Asia WGS
AF:
0.227
AC:
790
AN:
3478

ClinVar

Significance: protective
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Alzheimer disease, protection against Benign:1
protective, no assertion criteria providedliterature onlyOMIMAug 01, 2006- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.65
Dann
Benign
0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1800630; hg19: chr6-31542476; API